<div dir="ltr">Dear Jin,<div><br></div><div>You may want to check on a CTF Challenge we did a couple of years ago (Marabini et al. JSB 2015) for a more in depth analysis but, essentially, to assign a value to the astigmatism angle when your astigmatism is very small is not a very stable process. </div><div><br></div><div>Wbw..JM</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, May 30, 2017 at 3:55 PM, Marin van Heel <span dir="ltr"><<a href="mailto:marin.vanheel@googlemail.com" target="_blank">marin.vanheel@googlemail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
Hi Sjors and Jin,<br>
<br>
This type of anisotropy has a name: Astigmatism!<br>
It may sound pedantic but anisotropy in EM normally refers to a magnification anisotropy, not to astigmatism.<br>
<br>
Cheers,<br>
<br>
Marin<br>
<br>
<br>
On 29/05/2017 18:51, Sjors Scheres wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Jin,<br>
In the case of anisotropy your Thon rings are elliptical instead of<br>
circular because the defocus in one direction (defocusU) is not the same<br>
as the defocus in the perpendicular direction (defocusV). DefocusAngle<br>
describes the direction of this anisotropy. It is defined as the angle<br>
between defocusU and the X-axis (if I remember correctly...). Both<br>
ctffind4 and gctf estimate anisotropy for every micrograph, but if your<br>
microscope was well aligned, then you may have hardly any anisotropy in<br>
the data. This will result in very similar defocusU and defocusV values<br>
for each micrograph. In that case, defocusAngle doesn't mean anything, and<br>
can vary wildly between the different programs. I suspect this is what is<br>
happening, but you can just check by plotting defocusU values against<br>
defocusV values for the entire dataset. I suspect you can mix your<br>
particles as you want without large effects on the reconstruction.<br>
HTH,<br>
Sjors<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi All,<br>
<br>
This may be very trivial thing. I am going to combine particles from two<br>
dataset. And each dataset was processed with ctffind4 and gctf. I found<br>
each program gives similar defocus values but different defocus angles per<br>
image. What does defocus angle do in CTF and would it be okay to combine<br>
the data from different softwares?<br>
<br>
Thanks in advance,<br>
<br>
Jin<br>
<br>
</blockquote>
<br>
</blockquote>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div>Prof. Jose-Maria Carazo<br>Biocomputing Unit, Head, CNB-CSIC<br>Spanish National Center for Biotechnology</div><div>Darwin 3, Universidad Autonoma de Madrid</div><div>28049 Madrid, Spain</div><div><p style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif"><br></p>Cell: +34639197980<br></div></div></div>
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